.TH g_dipoles 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_dipoles - computes the total dipole plus fluctuations

.B VERSION 4.5
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "\-en" " ener.edr "
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-o" " Mtot.xvg "
.BI "\-eps" " epsilon.xvg "
.BI "\-a" " aver.xvg "
.BI "\-d" " dipdist.xvg "
.BI "\-c" " dipcorr.xvg "
.BI "\-g" " gkr.xvg "
.BI "\-adip" " adip.xvg "
.BI "\-dip3d" " dip3d.xvg "
.BI "\-cos" " cosaver.xvg "
.BI "\-cmap" " cmap.xpm "
.BI "\-q" " quadrupole.xvg "
.BI "\-slab" " slab.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-mu" " real "
.BI "\-mumax" " real "
.BI "\-epsilonRF" " real "
.BI "\-skip" " int "
.BI "\-temp" " real "
.BI "\-corr" " enum "
.BI "\-[no]pairs" ""
.BI "\-ncos" " int "
.BI "\-axis" " string "
.BI "\-sl" " int "
.BI "\-gkratom" " int "
.BI "\-gkratom2" " int "
.BI "\-rcmax" " real "
.BI "\-[no]phi" ""
.BI "\-nlevels" " int "
.BI "\-ndegrees" " int "
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&g_dipoles computes the total dipole plus fluctuations of a simulation
\&system. From this you can compute e.g. the dielectric constant for
\&low dielectric media.
\&For molecules with a net charge, the net charge is subtracted at
\&center of mass of the molecule.


\&The file Mtot.xvg contains the total dipole moment of a frame, the
\&components as well as the norm of the vector.
\&The file aver.xvg contains  |Mu|2  and | Mu |2 during the
\&simulation.
\&The file dipdist.xvg contains the distribution of dipole moments during
\&the simulation
\&The mu_max is used as the highest value in the distribution graph.


\&Furthermore the dipole autocorrelation function will be computed when
\&option \-corr is used. The output file name is given with the \fB \-c\fR
\&option.
\&The correlation functions can be averaged over all molecules
\&(\fB mol\fR), plotted per molecule separately (\fB molsep\fR)
\&or it can be computed over the total dipole moment of the simulation box
\&(\fB total\fR).


\&Option \fB \-g\fR produces a plot of the distance dependent Kirkwood
\&G\-factor, as well as the average cosine of the angle between the dipoles
\&as a function of the distance. The plot also includes gOO and hOO
\&according to Nymand & Linse, JCP 112 (2000) pp 6386\-6395. In the same plot
\&we also include the energy per scale computed by taking the inner product of
\&the dipoles divided by the distance to the third power.


\&


\&EXAMPLES


\&g_dipoles \-corr mol \-P1 \-o dip_sqr \-mu 2.273 \-mumax 5.0 \-nofft


\&This will calculate the autocorrelation function of the molecular
\&dipoles using a first order Legendre polynomial of the angle of the
\&dipole vector and itself a time t later. For this calculation 1001
\&frames will be used. Further the dielectric constant will be calculated
\&using an epsilonRF of infinity (default), temperature of 300 K (default) and
\&an average dipole moment of the molecule of 2.273 (SPC). For the
\&distribution function a maximum of 5.0 will be used.
.SH FILES
.BI "\-en" " ener.edr" 
.B Input, Opt.
 Energy file 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " Mtot.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-eps" " epsilon.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-a" " aver.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-d" " dipdist.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-c" " dipcorr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-g" " gkr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-adip" " adip.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-dip3d" " dip3d.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cos" " cosaver.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cmap" " cmap.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-q" " quadrupole.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-slab" " slab.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-mu"  " real" " \-1    " 
 dipole of a single molecule (in Debye)

.BI "\-mumax"  " real" " 5     " 
 max dipole in Debye (for histrogram)

.BI "\-epsilonRF"  " real" " 0     " 
 epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)

.BI "\-skip"  " int" " 0" 
 Skip steps in the output (but not in the computations)

.BI "\-temp"  " real" " 300   " 
 Average temperature of the simulation (needed for dielectric constant calculation)

.BI "\-corr"  " enum" " none" 
 Correlation function to calculate: \fB none\fR, \fB mol\fR, \fB molsep\fR or \fB total\fR

.BI "\-[no]pairs"  "yes   "
 Calculate |cos theta| between all pairs of molecules. May be slow

.BI "\-ncos"  " int" " 1" 
 Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the \-gkr flag.

.BI "\-axis"  " string" " Z" 
 Take the normal on the computational box in direction X, Y or Z.

.BI "\-sl"  " int" " 10" 
 Divide the box in nr slices.

.BI "\-gkratom"  " int" " 0" 
 Use the n\-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors

.BI "\-gkratom2"  " int" " 0" 
 Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules

.BI "\-rcmax"  " real" " 0     " 
 Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used.

.BI "\-[no]phi"  "no    "
 Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the xpm file from the \-cmap option. By default the cosine of the angle between the dipoles is plotted.

.BI "\-nlevels"  " int" " 20" 
 Number of colors in the cmap output

.BI "\-ndegrees"  " int" " 90" 
 Number of divisions on the y\-axis in the camp output (for 180 degrees)

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
